SARS-CoV-2 Lineage Variant Summary


Nucleotide variants related to lineages of concern and observed in > 10% of sequences are indicated in yellow above a schematic SARS-CoV-2 genome. Primers that do not overlap with variants associated with these lineages are shown in blue. Overlapping primers are indicated in orange.

Overlapping amplicons:


0-5 kb Variants


5-10 kb Variants


10-15 kb Variants


15-20 kb Variants


20-25 kb Variants


25-29 kb Variants


Methods:

Sequences reported in Sequence Sources for each lineage were aligned to the NC_045512.2 reference sequence (minimap2). Variants > 10% frequency (freebayes) were evaluated for overlap with primer regions (bedtools) and displayed (Geneious Prime 2021.0.3).


Sequence Sources:

B.1.617.2: GitHub. “Potential Sequences That Should Be Included in B.1.617 · Issue #49 · Cov-Lineages/Pango-Designation.” Accessed June 20, 2021. https://github.com/cov-lineages/pango-designation/issues/49.

AY.3: GitHub. “B.1.617.2 Sub-Lineage with ORF1a: I3731V · Issue #121 · Cov-Lineages/Pango-Designation.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/issues/121.

AY.4: GitHub. “Proposal for Sub-Lineages within B.1.617.2 · Issue #180 · Cov-Lineages/Pango-Designation.” Accessed October 1, 2021. https://github.com/cov-lineages/pango-designation/issues/180.

AY.4.2: GitHub. “Proposal for AY.4 Sublineage with S:145H + S:222V (Mostly UK) · Issue #223 · Cov-Lineages/Pango-Designation.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/issues/223.

AY.25: GitHub. “B.1.617.2 Sublineage with Expansion in Cape Cod, Massachusetts, USA in July 2021 · Issue #181 · Cov-Lineages/Pango-Designation.” Accessed October 1, 2021. https://github.com/cov-lineages/pango-designation/issues/181.

AY.43: GitHub. “Proposal for Large European Delta Sub-Lineage with N:9L, ORF1b:829I (~80k Seqs) · Issue #240 · Cov-Lineages/Pango-Designation.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/issues/240.

AY.44: GitHub. “Proposal for Large US Delta Sub-Lineage with Orf1b:183V (~80k Sequences) · Issue #242 · Cov-Lineages/Pango-Designation.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/issues/242.

AY.100: GitHub. “Added New Lineage AY.100 with 129 New Sequence Designations · Cov-Lineages/Pango-Designation@f792f5d.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/commit/0892b9f7e2f19f7f8d9e655de277083747b267e1.

AY.103: GitHub. “Added New Lineage AY.103 with 18135 New Sequence Designations and 13 … · Cov-Lineages/Pango-Designation@0892b9f.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/commit/0892b9f7e2f19f7f8d9e655de277083747b267e1.

AY.119: GitHub. “Added New Lineage AY.119 with 2928 New Sequence Designations and 13 U… · Cov-Lineages/Pango-Designation@47fe370.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/commit/47fe3701bd6fa4699f47133212945e2710e7e301.

B.1.1.529 (omicron): GitHub. “B.1.1 decendant associated with Southern Africa with high number of Spike mutations · Issue #343 · Cov-Lineages/Pango-Designation.” Accessed November 27, 2021. https://github.com/cov-lineages/pango-designation/issues/343.


Amplicon Designs:

US CDC: Lu, Xiaoyan, Lijuan Wang, Senthilkumar K. Sakthivel, Brett Whitaker, Janna Murray, Shifaq Kamili, Brian Lynch, et al. “US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 - Volume 26, Number 8—August 2020 - Emerging Infectious Diseases Journal - CDC.” Accessed April 23, 2021. https://doi.org/10.3201/eid2608.201246.

China CDC: “新型冠状病毒核酸检测引物和探针序列(Specific Primers and Probes for Detection 2019 Novel Coronavirus).” Accessed June 20, 2021. http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html.

Charité: Corman, Victor M., Olfert Landt, Marco Kaiser, Richard Molenkamp, Adam Meijer, Daniel KW Chu, Tobias Bleicker, et al. “Detection of 2019 Novel Coronavirus (2019-NCoV) by Real-Time RT-PCR.” Eurosurveillance 25, no. 3 (January 23, 2020): 2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045a.

ARTIC v3: Tyson, John R., Phillip James, David Stoddart, Natalie Sparks, Arthur Wickenhagen, Grant Hall, Ji Hyun Choi, et al. “Improvements to the ARTIC Multiplex PCR Method for SARS-CoV-2 Genome Sequencing Using Nanopore.” BioRxiv: The Preprint Server for Biology, September 4, 2020. https://doi.org/10.1101/2020.09.04.283077.

Midnight 1200 bp: Freed, Nikki E., Markéta Vlková, Muhammad B. Faisal, and Olin K. Silander. “Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using 1200 Bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding.” Biology Methods & Protocols 5, no. 1 (2020): bpaa014. https://doi.org/10.1093/biomethods/bpaa014.

ARTIC v4: ARTIC Real-time Genomic Surveillance. “SARS-CoV-2 Version 4 Scheme Release - Laboratory,” June 24, 2021. https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312.

VarSkip: VarSkip Multiplex PCR Designs for SARS-CoV-2 Sequencing. 2021. Reprint, New England Biolabs Inc., 2021. https://github.com/nebiolabs/VarSkip.


Software Tools:

Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. https://doi.org/10.1093/bioinformatics/bty191 .

Garrison, Erik, and Gabor Marth. “Haplotype-Based Variant Detection from Short-Read Sequencing.” ArXiv:1207.3907 [q-Bio], July 20, 2012. http://arxiv.org/abs/1207.3907.

Quinlan, Aaron R, and Ira M Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics (Oxford, England) 26 (2010): 841–42. https://doi.org/10.1093/bioinformatics/btq033 .

Geneious version 2021.1 created by Biomatters. Available from https://www.geneious.com


History:

2021-11-29: added missing diagnostic tests

2021-11-27: added currently circulating lineages, new primer overlap visualization

2021-10-07: removed duplicate VarSkip amplicon 61

2021-09-29: Added VarSkip, removed new VBM lineages

2021-06-24: Added ARTICv4

2021-06-20: Updated to currently relevant variants of concerns.